This invention relates to the manufacture of supports having bound to the surfaces thereof a plurality of chemical compounds, such as biopolymers. In particular, the invention relates to cutting of sheets of material that comprise multiple supports into individual assay devices, each comprising a single support.
In the field of diagnostics and therapeutics, it is often useful to attach species to a surface. One important application is in solid phase chemical synthesis wherein initial derivatization of a substrate surface enables synthesis of polymers such as oligonucleotides and peptides on the substrate itself. Support bound oligomer arrays, particularly oligonucleotide arrays, may be used in screening studies for determination of binding affinity. Modification of surfaces for use in chemical synthesis has been described. See, for example, U.S. Pat. No. 5,624,711 (Sundberg), U.S. Pat. No. 5,266,222 (Willis) and U.S. Pat. No. 5,137,765 (Farnsworth).
Determining the nucleotide sequences and expression levels of nucleic acids (DNA and RNA) is critical to understanding the function and control of genes and their relationship, for example, to disease discovery and disease management. Analysis of genetic information plays a crucial role in biological experimentation. This has become especially true with regard to studies directed at understanding the fundamental genetic and environmental factors associated with disease and the effects of potential therapeutic agents on the cell. Such a determination permits the early detection of infectious organisms such as bacteria, viruses, etc.; genetic diseases such as sickle cell anemia; and various cancers. This paradigm shift has lead to an increasing need within the life science industries for more sensitive, more accurate and higher-throughput technologies for performing analysis on genetic material obtained from a variety of biological sources.
Unique or misexpressed nucleotide sequences in a polynucleotide can be detected by hybridization with a nucleotide multimer, or oligonucleotide, probe. Hybridization is based on complementary base pairing. When complementary single stranded nucleic acids are incubated together, the complementary base sequences pair to form double stranded hybrid molecules. These techniques rely upon the inherent ability of nucleic acids to form duplexes via hydrogen bonding according to Watson-Crick base-pairing rules. The ability of single stranded deoxyribonucleic acid (ssDNA) or ribonucleic acid (RNA) to form a hydrogen bonded structure with a complementary nucleic acid sequence has been employed as an analytical tool in molecular biology research. An oligonucleotide probe employed in the detection is selected with a nucleotide sequence complementary, usually exactly complementary, to the nucleotide sequence in the target nucleic acid. Following hybridization of the probe with the target nucleic acid, any oligonucleotide probe/nucleic acid hybrids that have formed are typically separated from unhybridized probe. The amount of oligonucleotide probe in either of the two separated media is then tested to provide a qualitative or quantitative measurement of the amount of target nucleic acid originally present.
Direct detection of labeled target nucleic acid hybridized to surface-bound polynucleotide probes is particularly advantageous if the surface contains a mosaic of different probes that are individually localized to discrete, and often known, areas of the surface. Such ordered arrays containing a large number of oligonucleotide probes have been developed as tools for high throughput analyses of genotype and gene expression. Oligonucleotides synthesized on a solid support recognize uniquely complementary nucleic acids by hybridization, and arrays can be designed to define specific target sequences, analyze gene expression patterns or identify specific allelic variations. The arrays may be used for conducting cell study, diagnosing disease, identifying gene expression, monitoring drug response, determination of viral load, identifying genetic polymorphisms, analyzing gene expression patterns or identifying specific allelic variations, and the like.
In one approach, cell matter is lysed, to release its DNA as fragments, which are then separated out by electrophoresis or other means, and then tagged with a fluorescent or other label. The resulting DNA mix is exposed to an array of oligonucleotide probes, whereupon selective binding to matching probe sites takes place. The array is then washed and interrogated to determine the extent of hybridization reactions. In one approach the array is imaged so as to reveal for analysis and interpretation the sites where binding has occurred. Arrays of different chemical compounds or moieties or probe species provide methods of highly parallel detection, and hence improved speed and efficiency, in assays. Assuming that the different sequence polynucleotides were correctly deposited in accordance with the predetermined configuration, then the observed binding is indicative of the presence and/or concentration of one or more polynucleotide components of the sample.
The arrays may be microarrays created on the surface of a support by in situ synthesis of biopolymers such as polynucleotides, polypeptides, polysaccharides, etc., and combinations thereof, or by deposition of molecules such as oligonucleotides, cDNA and so forth. In general, arrays are synthesized on a surface of a support or substrate by one of any number of synthetic techniques that are known in the art. In one approach, for example, the support may be one on which a single array of chemical compounds is synthesized. Alternatively, multiple arrays of chemical compounds may be synthesized on the support, which is then diced, i.e., cut, into individual assay devices, which are supports that each comprise a single array, or in some instances multiple arrays, on a surface of the support.
Brittle materials such as glass are often cut into individual pieces by using a technique wherein the sheet of material is scored transversely to produce a crack and, then, the sheet is mechanically stressed in such a manner that strips are broken from the sheet along the score lines. This process is sometimes referred to as the “scribe and break” method. The mechanical stressing may be accomplished in a number of known ways. Generally, the scored material is placed in three or four point bending in the scored area. The sheet is flexed such that the scored side of the material is put in tension, thus, propagating the crack through the material. The process has been automated. Cutting lines are provided on the surface of the glass sheet by, for example, a cutter. Push rollers are applied to the parts just outside the cutting lines and support rollers are applied to the back of the glass sheet and at the parts just inside the cutting lines. Force is applied to the glass by means of the push rollers to bend and break the glass sheet along the cutting lines. In a conventional glass cutting apparatus a roller conveyor is provided on a stationary frame and push rollers for breaking off the sheet glass and support rollers are also mounted on the frame.
The common methods of breaking sheet materials into pieces of predetermined size have difficulties when applied to supports that have chemical compounds on their surfaces, particularly, biopolymers in the form of arrays. When the process is performed automatically, it involves fixing the material in a tool where force is applied to both sides of the score or scribe on the material while a reaction force is applied to the area of the score from the unscored side or surface. The method requires the material to be moved into position, fixed in position, broken and then removed from the cutting area. Another problem with the common methods is control of the single cut pieces. Where the pieces do not have identical chemical or biological coatings, they must be handled in such a way to assure that the identity of the single pieces is not lost. Furthermore, most breaking operations are not suitable for handling and snapping the brittle material without touching the surfaces of the material. When the surfaces contain fragile coatings such as arrays of chemical compounds, contamination of and/or damage to the surface of the supports can occur.
There is, therefore, a need for methods and apparatus for cutting sheets of brittle material into single pieces where the surface of the sheets comprises multiple arrays of chemical compounds. The methods and apparatus should permit continuous, high speed processing and provide control of the single pieces cut from the sheet.